The secondary structure of the wild type Paracoccus denitrificans cytochrome c oxidase obtained by decomposition of the infrared amide I band contains 44% a-helix, 18% b-sheet, 14% turns, 18% loops and 6% non-ordered segments. The mutant lacking subunit III presents a small but significant increase (~6%) in the percentage of loops and slight differences in the other components. Using band/area ratios and tyrosine side chain absorption as inner standard it is shown that in the absence of subunit III the structure of subunits I and II is altered , although no changes in a-helix or b-sheet content are observed. Thermal infrared studies show a complex denaturation pattern characterized by the presence of a partially denatured intermediate state. Of the seven predicted subunit III a helices, only four appear to be resistant to thermal perturbation, suggesting that this is the number of transmembrane helices in subunit III. These FTIR data are confirmed by the thermodynamic data based on the calorimetric results.